I also looked into this issue a lot and I sent my results through to MattW who said BigAnt will look into a fix soon but here's what I found/sent to him (It's long but detailed):
Hey Matt,
As you know myself and many others have a problem where there are duplicates of players in our careers when there aren't any duplicates in our academy. I have find out why there are duplicates but I don't know how to fix it. This is the stuff I found out:
^^^^This is Mitchell Starc's on disk linked player, Martin Samson (Note there is only one). The academy in this is completely reset and no teams/players/etc have been downloaded. He is attached to NSW, Sixers (Maximum), Australia, and Crowns. I am looking at Samson from the "Copy player appearance from career" option when you start a career mode which allows you to view every player that will be in the career mode(I know that you more then likely already know that feature but it's easier for me if I just explain everything so I don't miss anything), which is this image below.
What I did next is replace a few teams in the academy (Australia, South Africa, New Zealand and NSW) all of which were correctly linked. I double checked too make sure there were no duplicates in the academy and then started a new career. I checked in the same section as last time for which players were in the career and when I searched for starc in this section this is what it showed.
As you can see, there are now three different starcs all unlinked, all attached to a different team. Obviously it should be one starc who is attached to all teams and is linked. What I think has happened is that when the players in the teams are downloaded, even if I press "Replace current with new" (Which I did for Australia after I had already downloaded NSW) the player won't actually be replaced, instead the new version will be seen by the academy as a separate player. It's also important to note that the Mitchell Starc who in the photo above says he is playing for "Maximum" and "Crwons". These are the two teams that starc is attached to that I did not download. Which kind of proves my theory on why he is being duplicated. Keep in mind this is all looking at starc through the career mode search not the academy search. In the academy there is one mitch starc who is linked and attached to all the necessary clubs.
Another thing to note is that on the academy, starc is rated 88 yet on career it says he is 89, which is another error caused by the connection between the academy and career.
I tried to remove starc from all his attached teams and then add him back in the academy hoping it would kind of reset him in career. Instead in the career search, it just made 4 copies of him all attached to a single one of his teams except this time they were all linked. Shown in the photo below.
Another thing that proves this (which I don't have photos of sadly) is that Hashim Amla who is only attached to one club (South Africa and their ATB but of course ATB is not in career) shows up in the career search as a linked player attached to South Africa.
Basically the issue is when the academy is telling you that your downloaded player is linked and attached to all his teams, but when you start your career, there is actually multiple versions of that player all attached to ONE team. This would obviously lead to having duplicates of high rated players such as mitch starc in the aussie team as not only is he already in the BBl(Sixers) and australian domestic comps (NSW) which makes the career mode think that they are 3 completely different players, hence selects all of them due to they're high ratings and people who play career end up having three mitch starcs or whoever else. It also works with Steve smith except most people have two of him as he belongs to NSW and Australia, but not a BBl club.
Hope this info is helpful and makes sense (I know it's long but I wanted to be thorough) and that this can be fixed soon.
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the Big Bash were particularly bad ... I could not even start a custom game if they had their logos!
it took 2 hours for this clean up, and I had to restart career. Till now no duplicates after the redownload.
